Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9db3f56bbe70ea3d578d16985c5c38c73ec5e42 https://github.com/galaxyproject/galaxy/commit/c9db3f56bbe70ea3d578d16985c5c... Author: Christian-B github@brenn.co.uk Date: 2015-11-23 (Mon, 23 Nov 2015)
Changed paths: M lib/galaxy/datatypes/tabular.py
Log Message: ----------- Alternative stricter csv formats
Commit: fa7ccdf4b07598f5ebdfb1400f0bec2e2dabc164 https://github.com/galaxyproject/galaxy/commit/fa7ccdf4b07598f5ebdfb1400f0be... Author: Christian-B github@brenn.co.uk Date: 2015-11-23 (Mon, 23 Nov 2015)
Changed paths: M lib/galaxy/datatypes/tabular.py
Log Message: ----------- Flake8 fix
Commit: 79a7e31da7e6151c64b32f911fc60fcbdb78bba2 https://github.com/galaxyproject/galaxy/commit/79a7e31da7e6151c64b32f911fc60... Author: Christian-B github@brenn.co.uk Date: 2015-11-23 (Mon, 23 Nov 2015)
Changed paths: M lib/galaxy/datatypes/tabular.py
Log Message: ----------- Remove bug log statement
Commit: 7a960b08521ffa00e2984434aa870a49a96da0b5 https://github.com/galaxyproject/galaxy/commit/7a960b08521ffa00e2984434aa870... Author: John Chilton jmchilton@gmail.com Date: 2016-01-04 (Mon, 04 Jan 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py
Log Message: ----------- Small tweaks to CSV fixes by @Christian-B.
- Update sample datatype conf. - Use Python naming conventions and PEP-8 style fixes.
Commit: 132ff18db68db6bd611dd94ed988d4c5f6d1dee5 https://github.com/galaxyproject/galaxy/commit/132ff18db68db6bd611dd94ed988d... Author: Christian Y. Brenninkmeijer christian.brenninkmeijer@manchester.ac.uk Date: 2016-01-05 (Tue, 05 Jan 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py
Log Message: ----------- Merge pull request #1 from jmchilton/csv_fix
Small tweaks to CSV fixes by @Christian-B.
Commit: de506dec0c52e655a3fdff96368a288b6c454cde https://github.com/galaxyproject/galaxy/commit/de506dec0c52e655a3fdff96368a2... Author: Christian-B github@brenn.co.uk Date: 2016-02-23 (Tue, 23 Feb 2016)
Changed paths: M lib/galaxy/datatypes/tabular.py
Log Message: ----------- fixed spelling found by @nsoranzo
Commit: 7e0427b8b7d0f3de78175d254baff058bb0fce28 https://github.com/galaxyproject/galaxy/commit/7e0427b8b7d0f3de78175d254baff... Author: John Chilton jmchilton@gmail.com Date: 2016-03-01 (Tue, 01 Mar 2016)
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doc/source/admin/dependency_resolvers.rst A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst M doc/source/dev/faq.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/project/issues.rst M doc/source/project/organization.rst A doc/source/releases/15.10.rst M doc/source/releases/15.10_announce.rst A doc/source/releases/16.01.rst A doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/constructive_solid_geometry.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py A lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml A lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py A 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Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into csv_fix
Commit: b8cb5432a204742956267ba5b76f6eb4804983b4 https://github.com/galaxyproject/galaxy/commit/b8cb5432a204742956267ba5b76f6... Author: John Chilton jmchilton@gmail.com Date: 2016-03-01 (Tue, 01 Mar 2016)
Changed paths: M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/issue1818.tabular
Log Message: ----------- Add test for #1818 to PR #1156.
Commit: 5eb96a5fcf4ff8d521eeaa34172b5b72e902814b https://github.com/galaxyproject/galaxy/commit/5eb96a5fcf4ff8d521eeaa34172b5... Author: John Chilton jmchilton@gmail.com Date: 2016-03-21 (Mon, 21 Mar 2016)
Changed paths: M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/onload.js M client/galaxy/style/less/base.less M client/galaxy/style/less/library.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/grunt-tasks/style.js M client/package.json M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/tool_conf.xml.main M config/tool_data_table_conf.xml.sample M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init M create_db.sh A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M doc/source/admin/framework_dependencies.rst M lib/galaxy/app.py M lib/galaxy/config.py A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/datatypes/display_applications/application.py A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/form_builder.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/api/categories.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/tool_shed_registry.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/metadata_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py M manage_db.sh M manage_tools.sh M run.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/tours.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/tool/tool-form-workflow.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/tours.js M static/scripts/mvc/workflow/workflow-canvas.js M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/display.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M test/unit/workflows/test_modules.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample M tools/data_source/upload.py
Log Message: ----------- Merge PR #1156 into dev and fix #1818.
Commit: 0029949ed2ead12735ce052aca328cc783139da6 https://github.com/galaxyproject/galaxy/commit/0029949ed2ead12735ce052aca328... Author: John Chilton jmchilton@gmail.com Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py
Log Message: ----------- More fixups for specialized, more correct tabular datatypes.
Followed through with @nsoranzo's comment:
1. overwrite CSV.sniff() and CSV.set_meta() methods with the ones from BaseCSV 2. remove BaseCSV class and rename CSV to BaseCSV 3. rename ExcelCSV class to CSV
Also renamed ExcelTSV to TSV and corrected another bug in sample datatypes noticed by @nsoranzo.
Commit: a85d6d556655bb3cc83270c41e9628488613600d https://github.com/galaxyproject/galaxy/commit/a85d6d556655bb3cc83270c41e962... Author: Nicola Soranzo nsoranzo@tiscali.it Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/issue1818.tabular
Log Message: ----------- Merge pull request #1968 from jmchilton/csv_fix
Improve tabular datatypes.
Compare: https://github.com/galaxyproject/galaxy/compare/7129726e8fca...a85d6d556655